Variant report

Variant	rs9854590
Chromosome Location	chr3:23292600-23292601
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 123 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:118)

rs_ID	r²[population]
rs1013460	0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs1027379	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1032499	0.83[CHB][hapmap];0.89[JPT][hapmap]
rs11129113	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11129116	1.00[CEU][hapmap];0.94[CHB][hapmap];0.86[JPT][hapmap];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11708117	0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11708176	0.94[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11717397	0.86[ASN][1000 genomes]
rs11720461	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11920019	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12330262	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12330479	0.94[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.87[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs12493361	1.00[CEU][hapmap];0.89[CHB][hapmap];0.95[JPT][hapmap];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12496983	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12497974	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12629848	0.81[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13074192	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs13080261	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13080401	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13081371	0.96[AFR][1000 genomes];0.86[AMR][1000 genomes];0.80[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13321359	0.87[CHB][hapmap];0.81[JPT][hapmap]
rs13326048	0.89[CHB][hapmap];0.95[JPT][hapmap]
rs1353322	0.89[YRI][hapmap]
rs1495131	1.00[CEU][hapmap];0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1532355	0.81[ASN][1000 genomes]
rs1552930	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1692617	0.88[CHB][hapmap];0.85[JPT][hapmap]
rs1692651	0.89[CHB][hapmap];0.82[JPT][hapmap]
rs1695171	0.89[CHB][hapmap]
rs1695200	0.81[JPT][hapmap]
rs17012812	1.00[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17012869	1.00[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1973400	0.94[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2055154	0.97[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs2172828	0.81[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2359759	0.89[CHB][hapmap];0.95[JPT][hapmap];0.90[YRI][hapmap]
rs2359763	0.89[CHB][hapmap];0.81[JPT][hapmap]
rs2884731	0.80[YRI][hapmap]
rs3104243	0.89[CHB][hapmap];0.81[JPT][hapmap]
rs34919006	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4241511	1.00[CEU][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4241512	0.83[ASN][1000 genomes]
rs4488778	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4858062	0.80[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4858064	0.98[AFR][1000 genomes];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4858074	0.83[YRI][hapmap]
rs4858483	0.95[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4858484	1.00[CEU][hapmap];0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4858491	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4858492	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4858496	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4858497	1.00[CEU][hapmap];0.94[CHB][hapmap];0.81[JPT][hapmap];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4858500	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4858501	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4858502	1.00[CEU][hapmap];0.89[CHB][hapmap];0.95[JPT][hapmap];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4858504	0.82[YRI][hapmap];0.84[ASN][1000 genomes]
rs4858506	0.89[CHB][hapmap];0.95[JPT][hapmap]
rs4858509	0.82[ASN][1000 genomes]
rs59429714	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6550746	0.94[CHB][hapmap];0.95[JPT][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6550748	1.00[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6550755	0.89[CHB][hapmap];0.90[JPT][hapmap]
rs6550756	0.89[CHB][hapmap];0.81[JPT][hapmap];0.93[YRI][hapmap]
rs6769173	0.89[CHB][hapmap];0.81[JPT][hapmap];0.90[YRI][hapmap]
rs6780723	0.91[JPT][hapmap]
rs6784195	0.89[CHB][hapmap];0.95[JPT][hapmap]
rs6784771	0.83[CEU][hapmap];0.94[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6795492	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6795968	0.81[YRI][hapmap]
rs6796840	0.89[CHB][hapmap];0.81[JPT][hapmap]
rs6804123	1.00[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];0.83[YRI][hapmap];0.82[AFR][1000 genomes];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6805889	0.95[CHB][hapmap];0.95[JPT][hapmap];0.97[YRI][hapmap];0.83[ASN][1000 genomes]
rs6808513	0.82[JPT][hapmap]
rs704533	0.81[JPT][hapmap]
rs716457	0.89[CHB][hapmap];0.82[JPT][hapmap]
rs7429470	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7617072	0.83[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7622784	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7631334	0.89[CHB][hapmap];0.95[JPT][hapmap];0.90[YRI][hapmap]
rs778459	0.89[CHB][hapmap];0.82[JPT][hapmap]
rs778460	0.89[CHB][hapmap];0.81[JPT][hapmap];0.87[YRI][hapmap]
rs778462	0.89[CHB][hapmap];0.81[JPT][hapmap]
rs778468	0.89[CHB][hapmap];0.95[JPT][hapmap]
rs778470	0.89[CHB][hapmap];0.81[JPT][hapmap]
rs778471	0.89[CHB][hapmap];0.82[JPT][hapmap]
rs778486	0.89[CHB][hapmap];0.81[JPT][hapmap]
rs778494	0.89[CHB][hapmap];0.95[JPT][hapmap];0.87[YRI][hapmap]
rs778499	0.82[JPT][hapmap]
rs778500	0.82[JPT][hapmap]
rs778506	0.89[CHB][hapmap];0.81[JPT][hapmap]
rs778508	0.89[CHB][hapmap];0.85[JPT][hapmap]
rs9310715	1.00[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9809176	1.00[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];0.97[YRI][hapmap];0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9816895	0.93[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9821101	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9822422	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9825778	0.87[CHB][hapmap];0.95[JPT][hapmap]
rs9826647	0.89[CHB][hapmap];0.82[JPT][hapmap]
rs9826877	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9836787	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9839738	0.94[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.84[ASN][1000 genomes]
rs9841123	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9841944	0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9846398	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9847027	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9847958	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9848077	0.81[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.81[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs9849176	1.00[CEU][hapmap];0.83[CHB][hapmap];0.94[JPT][hapmap];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9853489	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9854148	0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9859651	0.89[CHB][hapmap];0.95[JPT][hapmap]
rs9861803	0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9864908	0.81[CEU][hapmap];0.89[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9865602	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9873317	0.81[CHB][hapmap];0.80[JPT][hapmap]
rs9874082	1.00[CEU][hapmap];0.89[CHB][hapmap];0.95[JPT][hapmap];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9874822	0.88[AFR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9881332	0.86[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv834636	chr3:23138653-23301443	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	nsv1014701	chr3:23257658-23416094	Weak transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
3	nsv589947	chr3:23277838-23403943	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	nsv1002823	chr3:23277838-23623083	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	nsv589948	chr3:23287141-23390221	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Strong transcription Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:23274800-23298200	Weak transcription	Aorta	Aorta
2	chr3:23281400-23298200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr3:23282200-23294600	Weak transcription	A549	lung
4	chr3:23283200-23296000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr3:23283600-23302200	Weak transcription	Left Ventricle	heart
6	chr3:23289000-23294800	Weak transcription	Skeletal Muscle Female	skeletal muscle
7	chr3:23290000-23292600	Weak transcription	Brain Angular Gyrus	brain
8	chr3:23290400-23295800	Weak transcription	Adipose Nuclei	Adipose
9	chr3:23290600-23298200	Weak transcription	Skeletal Muscle Male	skeletal muscle
10	chr3:23290800-23294800	Weak transcription	Primary B cells from peripheral blood	blood
11	chr3:23291600-23292800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr3:23291600-23298400	Weak transcription	Spleen	Spleen
13	chr3:23291800-23298200	Weak transcription	Thymus	Thymus
14	chr3:23292000-23293000	Enhancers	Brain Inferior Temporal Lobe	brain
15	chr3:23292200-23298800	Weak transcription	Primary T cells from cord blood	blood
16	chr3:23292400-23292800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr3:23292400-23292800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr3:23292400-23292800	Enhancers	Brain Anterior Caudate	brain
19	chr3:23292400-23292800	Enhancers	Duodenum Smooth Muscle	Duodenum
20	chr3:23292400-23293000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr3:23292400-23293000	Enhancers	Psoas Muscle	Psoas
22	chr3:23292400-23293600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
23	chr3:23292400-23293600	Enhancers	Brain Substantia Nigra	brain
24	chr3:23292400-23293800	Enhancers	Brain Cingulate Gyrus	brain
25	chr3:23292400-23296200	Enhancers	Brain Hippocampus Middle	brain
26	chr3:23292600-23292800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr3:23292600-23292800	Enhancers	Lung	lung
28	chr3:23292600-23292800	Enhancers	Pancreas	Pancrea
29	chr3:23292600-23292800	Enhancers	NHLF	lung
30	chr3:23292600-23293000	Enhancers	NH-A	brain
31	chr3:23292600-23293000	Enhancers	Osteobl	bone
32	chr3:23292600-23293200	Enhancers	Brain Angular Gyrus	brain
33	chr3:23292600-23295000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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